For libraries that meet submission guidelines and pass QC, we guarantee sequencing reads matching the specifications for our instruments.

NovaSeq X:

1 lane of a 10B or 1.5B flowcell lane will generate 1.2-1.5 billion reads per lane. We offer the 25B flowcell for large projects requiring at least 25 billion reads at ~2.5 billion reads per lane (enough to fill the flowcell).

Element Aviti:

Reads for the Element Aviti vary based on the run-type requested. Shorter run-types can expect ~500 million read while longer run-types can expect ~300 million reads.

Oxford Nanopore Promethion:

The platform can deliver around 500 GB of data per flowcell.

In order to guarantee high quality sequencing data, we conduct extensive QC on all client generated libraries entering our facility. Each QC step will consume library volume. Sequencing will consume yet more library, dependent on the amount of sequencing reads requested. Larger projects therefore will require a larger submission volume. Submission volumes also vary for QC services.

As a general guideline, we recommend the following submission volumes (at 10nM):
• For individual libraries that will be pooled at our facility: 13 μl at 10 nM
• For pre-pooled libraries: 20 μl at 10nM per billion reads requested
• For QC-only submissions: 3 ul per sample
• For Covaris shearing: 50-120 μl

We strive to offer the highest quality of service possible to the university of Chicago research community. As such we will do our best to accommodate submissions that fall outside of these suggested guidelines. While we pride ourselves on being able to sequence anything, we cannot guarantee optimal data output for submitted libraries with a concentration of <3 nM, though we can still try!

As sequencing has matured as a technology a higher emphasis is placed on lower costs, and shorter turn-around-times (TAT). While we are a small core, we strive to remain competitive on these fronts while still offering a large degree of flexibility and support to our clients.
In general, our turnaround time between sample submission and final data delivery is ~2-3 weeks. However, in practice turnaround time may vary due to several factors:

1) Project size and complexity:
Large and complex projects take longer to process than small simple projects. Projects requiring pooling of multiple samples in our facility will generally take additional time compared to pre-pooled or single library submissions.

2) Library composition:
Presence of primer and adapter dimers in the final sequencing pool can reduce data quality. As such we generally recommend that clients allow us to remove any residual dimer present in submitted libraries. This can add to project timelines, especially for small RNA libraries which require a more labor-intensive cleanup method. Libraries made using well validated protocols that leave little leftover dimer will generally lead to shorter turnaround times.

3) Requested run-type:
We must run the sequencer in an economical manner to be a viable core facility. Currently, for the NovaSeqX, the 8-lane 10B flowcell is the most cost-effective option for most clients and is what we run most days. This arrangement imposes a limitation since we need to accumulate at least 8 lanes worth of sequencing requests with similar run-types in order to run the sequencer on any given day. Our most common run-types are paired-end 150 bp and 10x RNA. Less common run-types take longer to accumulate in the facility, and contribute to longer and less predictable turnaround times. In order to address this issue, we have recently invested in a new sequencer, the Element Aviti. The Aviti offers equivalent data to illumina platforms in terms of quality, read length, and data output. However, it is a smaller instrument with two modules that can be started independently, allowing for much more flexible run-scheduling. It is therefore better tailored to a variety of less common sequencing run-types and we hope that this platform will help to reduce turnaround times for our clients. Additionally, when submitting for NovaSeqX sequencing, clients are now able to specify that the core use any run-type for sequencing, allowing us more flexibility.

We have recently started offering a rapid sequencing service with data delivery in as little as one business day (guaranteed data back within five business days). This service is offered at no extra costs but is only available for qualifying projects. Clients must purchase a full flowcell worth of sequencing (on any of our instruments), submit library pools that are ready for sequencing, and contact core staff at least 24 hours in advance of submission to confirm availability.

Besides these options, we will do our best to return data in cases where a project is time sensitive. If you need data back by a specific time, please email (bsdgenomicsconsult@uchicagomedicine.org).

Submission can be located here.

If you are unsure about what to fill out, or need advice about what options to choose for your sequencing project please send us an email at bsdgenomicsconsult@uchicagomedicine.org.

We will do our best to interpret forms that have small inconsistencies or missing fields, and will reach out to the client if there is any ambiguity that prevents us from proceeding with a project.

From time to time we receive questions about services we do not advertise. While we cannot offer an exhaustive list of all possible services, here are some common services we have been asked about in the past:

qPCR:
We do not currently offer qPCR as a QC only service and we no longer offer self service access to the qPCR instrument.

DNA/RNA extraction:
We will accept raw biological materials for DNA or RNA extraction on a case by case basis. Please email bsdgenomicsconsult@uchicagomedicine.org for a consultation.

Bio-informatics:
We do not offer bioinformatics services. Clients submitting for sequencing will receive demultiplexed FASTQ files and basic QC for data validation. If you need additional support, please contact the Bioinformatics Core.

Bead Cleanups and Gel Cuts:
We do not offer adapter cleanups except in the case of sequencing submissions (i.e., while we do perform cleanups routinely, we are not able to offer this as a standalone service).

Pricing for sequencing is calculated based on the amount of sequencing requested and the amount of sample processing needed to complete the project. Please see our pricing page for a detailed list of fees.

From time to time we receive questions about how we handle samples in lab. Our Quality Control (QC) pipeline is designed to handle a wide variety of library types, submission volumes, and varying sample quality. If it can be sequenced, we will sequence it! Sample volume is preserved by design and we always keep a significant portion of your original sample if at all possible. We offer in-house size selection to remove unwanted material (i.e. dimers). QC is one of the biggest determinants of project timelines, so sample-sets that do not require size selection or need fewer rounds of QC tend to move through the facility faster.

Yes!

Our QC and sequencing pipeline preserve volume by design. In other words, we typically do not use all of a client’s original submission in sequencing, and we store all material associated with the project for some time. If you want to retrieve your samples, please email Genomics@bsd.uchicago.edu.

For sequencing submissions, we guarantee storage at our facility for three months. For QC only submission, we guarantee storage for two weeks. If you think you may want to request sequencing for previous QC only submission, please let us know as soon as possible to ensure they are not discarded.

Please drop off samples in the freezer outside room 1230C in the Knapp Center for Biological Discovery (KCBD). The genomics core freezer is next to the ice machine.

Address:

900 E 57th St,1230C

Chicago, IL 60637

If you have any additional questions or want to set up a consultation, please email bsdgenomicsconsult@uchicagomedicine.org